Blood pressure loci identified with a gene-centric array

Abstract

Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a bespoke gene-centric array to genotype an independent discovery sample of 25,118 individuals that combined hypertensive case-control and general population samples. We followed up four SNPs associated with BP at our p < 8.56 × 10(-7) study-specific significance threshold and six suggestively associated SNPs in a further 59,349 individuals. We identified and replicated a SNP at LSP1/TNNT3, a SNP at MTHFR-NPPB independent (r(2) = 0.33) of previous reports, and replicated SNPs at AGT and ATP2B1 reported previously. An analysis of combined discovery and follow-up data identified SNPs significantly associated with BP at p < 8.56 × 10(-7) at four further loci (NPR3, HFE, NOS3, and SOX6). The high number of discoveries made with modest genotyping effort can be attributed to using a large-scale yet targeted genotyping array and to the development of a weighting scheme that maximized power when meta-analyzing results from samples ascertained with extreme phenotypes, in combination with results from nonascertained or population samples. Chromatin immunoprecipitation and transcript expression data highlight potential gene regulatory mechanisms at the MTHFR and NOS3 loci. These results provide candidates for further study to help dissect mechanisms affecting BP and highlight the utility of studying SNPs and samples that are independent of those studied previously even when the sample size is smaller than that in previous studies.

Figure 1

Quantile-Quantile Plots of Meta-Analysis Results Each panel shows common (MAF > 5% shown in blue) and low-frequency (MAF ≤ 5% shown in red) SNPs separately. Shaded regions are 99% probability envelopes for no association, which depend on the number of SNPs and hence are different sizes for common and low-frequency SNPs. The horizontal dashed line indicates our overall study-specific significance threshold p < 8.56 × 10⁻⁷.

Figure 2

Regional Association Plots for Eight SNPs that Were p < 8.56 × 10⁻⁷ for at Least One Phenotype in an Analysis of Combined Discovery and Follow-Up Data The top of each plot shows local pairwise LD patterns (r² = 0 in white; r² = 1 in red) and a fine-scale recombination rate map (cyan lines). The center of each plot shows association results from the discovery analysis only (to maintain an equal sample size for all points) for the five phenotypes analyzed (DBP in blue, MAP in magenta, PP in green, SBP in red, and HTN in yellow). The bottom of each plot shows positions of transcripts of known genes.

Figure 3

Heat Plot Showing Percentage of Phenotypic Variance Explained in All Available Data for the Eight SNPs Numeric values are percentage R² for continuous traits (DBP, SBP, MAP, PP) and Cox and Snell pseudo-R² for HTN. Each SNP explains less than 0.1% of phenotypic variance. Stars indicate significance levels adjusting for M_eff = 58409 tests: ^∗p ≤ 0.05/58,409, ^∗∗p ≤ 0.01/58,409, ^∗∗∗p ≤ 0.001/58,409.